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Kalita M, Yadav K, Archana A, Gopakumar TG, Vasudev PG, Ramapanicker R. Incorporation of phenylcarbonyl groups in the sidechain: A tool to induce ordered assembly of peptides on surfaces. J Pept Sci 2024:e3629. [PMID: 38898708 DOI: 10.1002/psc.3629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024]
Abstract
The possibility of introducing various functionalities on peptides with relative ease allows them to be used for molecular applications. However, oligopeptides prepared entirely from proteinogenic amino acids seldom assemble as ordered structures on surfaces. Therefore, sidechain modifications of peptides that can increase the intermolecular interactions without altering the constitution of a given peptide become an attractive route to self-assembling them on surfaces. We find that replacing phenylalanine residues with unusual amino acids that have phenylcarbonyl sidechains in oligopeptides increases the formation of ordered self-assembly on a highly ordered pyrolytic graphite surface. Peptides containing the modified amino acids provided extended long-range ordered assemblies, while the analogous peptides containing phenylalanine residues failed to form long-range assemblies. X-ray crystallographic analysis of the bulk structures of these peptides and the analogous peptides containing phenylalanine residues reveal that such modifications do not alter the secondary structure in crystals. It also reveals that the secondary hydrogen bonding interaction through phenylcarbonyl sidechains facilitates extended growth of the peptides on graphite.
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Affiliation(s)
- Mrinal Kalita
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Khushboo Yadav
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Archana Archana
- Molecular and Structural Biology Department, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | | | - Prema G Vasudev
- Molecular and Structural Biology Department, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Ramesh Ramapanicker
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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Arjariya R, Kaur G, Sen S, Verma S, Lackinger M, Gopakumar TG. Kinetic versus thermodynamic polymorph stabilization of a tri-carboxylic acid derivative at the solid-liquid interface. NANOSCALE 2023; 15:13393-13401. [PMID: 37539991 DOI: 10.1039/d3nr02031b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The carboxylic acid moiety gives rise to structural variability in surface-supported self-assembly due to the common expression of various H-bonding motifs. Self-assembly of 3-fold symmetric tricarboxylic acid derivatives on surfaces typically results in monolayer structures that feature the common 2-fold cyclic R22(8) H-bond motif for at least one of the carboxylic acid groups. Polymorphs that are exclusively based on 3-fold cyclic R33(12) H-bonds were predicted but remained elusive. Here, we show the emergence of such a superflower (SF) structure purely based on R33(12) H-bonds for L-benzene-1,3,5-tricarbonyl phenylalanine (L-BTA), a molecule derived from the well-studied trimesic acid (TMA). In contrast to TMA, L-BTA is not completely planar and is also equipped with additional functional groups for the formation of secondary intermolecular bonds. At the heptanoic acid-graphite interface we transiently observe a SF structure, which is dynamically converted into a chicken-wire structure that only exhibits R22(8) H-bonds. Interestingly, when using nonanoic acid as a solvent the initially formed SF structure remained stable. This unexpected behaviour is rationalized by accompanying force field simulations and experimental determination of solvent-dependent L-BTA solubility.
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Affiliation(s)
- Richa Arjariya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, UP-208016, India.
| | - Gagandeep Kaur
- Department of Chemistry, College of Arts and Sciences, Howard University, Washington, DC-20059, USA
| | - Shantanu Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, UP-208016, India.
| | - Sandeep Verma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, UP-208016, India.
- Center for Nanoscience, Indian Institute of Technology Kanpur, Kanpur, UP-208016, India
| | - Markus Lackinger
- Department of Physics, Technical University of Munich, James-Franck-Strasse 1, Garching 85748, Germany
- Deutsches Museum, Museumsinsel 1, Munich 80538, Germany
| | - Thiruvancheril G Gopakumar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, UP-208016, India.
- Center for Nanoscience, Indian Institute of Technology Kanpur, Kanpur, UP-208016, India
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Biondi B, Formaggio F, Toniolo C, Peggion C, Crisma M. Isolated α-turns in peptides: a selected literature survey. J Pept Sci 2023:e3476. [PMID: 36603599 DOI: 10.1002/psc.3476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
The results of classifying into various types the 68 examples of isolated α-turns in the X-ray diffraction crystal structures of peptides documented in the literature are presented and discussed in this review article. α-Turns characterized by the trans disposition of all ω torsion angles are common for the backbone linear peptides investigated. In contrast, the cis arrangement of the N-terminal (ωi + 1 ) torsion angle, among those generated by the three residues internal to the α-turn, is a peculiar feature of 65% of the cyclic peptides. Among linear and cyclic peptides featuring the all-trans disposition of the ω torsion angles, only one third of the α-turns display φ,ψ values not too far from those characterizing regular α-helices. In general, our findings, taken together, suggest that a significant conformational diversity is compatible with the formation of an intramolecularly H-bonded C13 -member pseudocycle (α-turn) in linear and cyclic peptides.
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Affiliation(s)
- Barbara Biondi
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy
| | - Fernando Formaggio
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Claudio Toniolo
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Cristina Peggion
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Marco Crisma
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy
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Erratum. J Pept Sci 2019; 25:e3217. [DOI: 10.1002/psc.3217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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